7V6M | pdb_00007v6m

Crystal structure of lacto-N-biosidase TnX from Tynzenella nexilis, lacto-N-biose complex

• PDB DOI: https://doi.org/10.2210/pdb7V6M/pdb

• Classification: HYDROLASE
• Organism(s): Faecalimonas nexilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-08-20 Released: 2022-02-09 
• Deposition Author(s): Yamada, C., Fushinobu, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.209 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of glycoside hydrolase family 136 lacto-N-biosidases from monkey gut- and human adult gut bacteria.

Yamada, C., Katayama, T., Fushinobu, S.

(2022) Biosci Biotechnol Biochem 86: 464-475

• PubMed: 35092420 
• DOI: https://doi.org/10.1093/bbb/zbac015
• Primary Citation Related Structures: 
  7V6I, 7V6M


• PubMed Abstract: 
  

  Glycoside hydrolase family 136 (GH136) was established after the discovery and structural analysis of lacto-N-biosidase (LNBase) from the infant gut bacterium Bifidobacterium longum subsp. longum JCM1217 (BlLnbX). Homologous genes of BlLnbX are widely distributed in the genomes of human gut bacteria and monkey Bifidobacterium spp., although only 2 crystal structures were reported in the GH136 family. Cell suspensions of Bifidobacterium saguini, Tyzzerella nexilis, and Ruminococcus lactaris exhibited the LNBase activity. Recombinant LNBases of these 3 species were functionally expressed with their specific chaperones in Escherichia coli, and their kinetic parameters against p-nitrophenol substrates were determined. The crystal structures of the LNBases from B. saguini and T. nexilis in complex with lacto-N-biose I were determined at 2.51 and 1.92 Å resolutions, respectively. These structures conserve a β-helix fold characteristic of GH136 and the catalytic residues, but they lack the metal ions that were present in BlLnbX.

---

Organizational Affiliation: 
• Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
Graduate School of Biostudies, Kyoto University, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.25 kDa 
• Atom Count: 4,856 
• Modeled Residue Count: 570 
• Deposited Residue Count: 587 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibronectin type III domain-containing protein	A	587	Faecalimonas nexilis	Mutation(s): 0  Gene Names: DXA47_02055

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G00056MO GlyCosmos: G00056MO GlyGen: G00056MO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.209 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.205	α = 90
b = 71.782	β = 90
c = 161.488	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Yamada, C., Fushinobu, S.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16J09251
Japan Society for the Promotion of Science (JSPS)	Japan	18K14388

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2022-04-06
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description